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Yorodumi- PDB-3i1c: Crystal Structure of a Novel Engineered Diels-Alderase: DA_20_00_A74I -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i1c | ||||||
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Title | Crystal Structure of a Novel Engineered Diels-Alderase: DA_20_00_A74I | ||||||
Components | Diisopropyl-fluorophosphatase | ||||||
Keywords | HYDROLASE / Beta-propeller / Metal-binding | ||||||
Function / homology | Function and homology information diisopropyl-fluorophosphatase / diisopropyl-fluorophosphatase activity / calcium ion binding Similarity search - Function | ||||||
Biological species | Loligo vulgaris (squid) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Lambert, A.R. / Stoddard, B.L. | ||||||
Citation | Journal: Science / Year: 2010 Title: Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Authors: Siegel, J.B. / Zanghellini, A. / Lovick, H.M. / Kiss, G. / Lambert, A.R. / St Clair, J.L. / Gallaher, J.L. / Hilvert, D. / Gelb, M.H. / Stoddard, B.L. / Houk, K.N. / Michael, F.E. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i1c.cif.gz | 80 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i1c.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 3i1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/3i1c ftp://data.pdbj.org/pub/pdb/validation_reports/i1/3i1c | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36102.016 Da / Num. of mol.: 1 Mutation: A74I, E21A, E37Y, N120A, D121Y, Y144F, R146I, M148L, F173A, N175A, T195Q, E225K, D229A, N272A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Loligo vulgaris (squid) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIG4, diisopropyl-fluorophosphatase |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.21 % |
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
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Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 29, 2009 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 15218 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→37.12 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.385 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.383 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→37.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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